1. Mapping Genes for SLE: A Paradigm for Human Disease? Stephen S. Rich, Ph.D. Department of Public Health Sciences Wake Forest University School of Medicine

2. Simple vs Complex Traits Simple Traits -rare -single gene (Mendelian) -severe mutations -large phenotypic effect Complex Traits -common -many genes (Oligogenic) -mild mutations -small phenotypic effect Complex trait mapping is the major challenge in human genetics

3. Difficulties in Complex Disease Identifying genes that contribute to susceptibility of complex disease difficult due to underlying biological mechanisms –Phenotypic heterogeneity –Genetic heterogeneity –Gene-environment interaction Limited study power to detect small effect susceptibility genes (QTLs) Available sample size for genetic studies

4. Gene - Environment Interaction

5. Gene - Environment Interaction: Complex Genetic Diseases Genetic/Host Susceptibility Presymptomatic Conditions (Risk Factors or Markers of Disease Susceptibility) Environmental Influences Symptomatic Disease (Reversible or Irreversible Changes in Organ Structure and Function)

6. Steps Towards Finding a Gene Identification of a population Clinical assessment Linkage analysis - genome screen Fine mapping and gene localization Gene identification / sequence variants Functional genomics: Gene expression

7. Issues in Clinical Assessment Disease phenotype definitions –medical history, evidence of sub-clinical outcome, and a confirmation through a clinical examination –outpatient clinic records with varying data –positive answer to the questions “Have you ever been diagnosed with...?” and “If yes, has this happened more than once?” Standardized questionnaires Standardized protocols Study coordination and training of staff Quality Control / Quality Assurance

8. Choices of a Population Representation –Isolated, admixed or inbred –Mixed, heterogeneous populations Family structure –Unrelated individuals –Families Parents and children Extended families (pedigrees) Source –Single ethnic group –Multiple ethnic groups

9. Example of Linkage Analysis

10. Affected Sib Pair Family a//bc//d a//c25% a//c 50% a//d or b//c 25% b//d

11. Systemic Lupus Erythematosus SLE is a chronic autoimmune inflammatory disease characterized by the production of pathogenic autoantibodies SLE is a clinically heterogeneous disease that affects a variety of organs such as joints, skin, blood and kidneys SLE disproportionately affects women (>90%) of child- bearing age Prevalence of SLE in the United States is estimated to be between 40 - 45 cases per 100,000 (Hochberg 1997)

12. Familiality of SLE SLE has a strong genetic component –Increased concordance rates among MZ twins (Deapen et al., 1992, Reichlin et al., 1992) –Increased risk to siblings ( S =10-20; Vyse and Todd, 1996) SLE does not exhibit simple Mendelian inheritance patterns and may involve –incomplete penetrance –phenocopies –genetic heterogeneity –polygenic inheritance –modifying environmental effects

13. Affected Relative Pair Collections Minnesota cohort –187 SLE sib pair families –6p11-21, 16q13, 14q21-23, 20p12.3 Oklahoma cohort –94 extended multiplex pedigrees –1q23, 13q32, 20q13, 1q31 Ethnic-specific effects

14. NPL Regression Analysis of Combined Genome Scan for SLE Chromosomal LOD-1 Region Nearest Marker LOD Interval Chr 1 @ 263 D1S27852.14 253-285 Chr 4 @ 21 D4S4033.65 11-28 Chr 4 @ 165 D4S23682.00 147-178 Chr 6 @ 68 D6S2410 4.90 61-80 Chr 6 @ 85 D6S10313.84 57-100 Chr 7 @ 27 D7S5072.47 6-37 Chr 16 @ 77 D16S3253/D16S5033.51 65-85 Chr 20 @ 62 D20S481/D20S1191.97 57-67

27. Combined Genome Scan for SLE Sample Similarities and Differences Chromosomal LOD Score Region Nearest Marker Combined MN OK Chr 1 @ 263 D1S27852.14 2.2 0.3 Chr 4 @ 21 D4S4033.65 1.8 1.9 Chr 4 @ 165 D4S23682.00 1.9 0.3 Chr 6 @ 68 D6S2410 4.90 4.3 1.0 Chr 6 @ 85 D6S10313.84 3.6 0.7 Chr 7 @ 27 D7S5072.47 1.5 1.0 Chr 16 @ 77 D16S3253/D16S5033.51 4.3 0.3 Chr 20 @ 62 D20S481/D20S1191.97 2.0 0.3

28. Combined Genome Scan for SLE Ethnic Differences LOD Score Chromosomal African Region Nearest Marker Combined American Caucasian Chr 1 @ 263 D1S27852.14 0.0 1.8 Chr 4 @ 21 D4S4033.65 0.0 4.5 Chr 4 @ 165 D4S23682.00 0.7 1.9 Chr 6 @ 68 D6S2410 4.90 1.6 2.6 Chr 6 @ 85 D6S10313.84 2.5 1.4 Chr 7 @ 27 D7S5072.47 0.0 2.9 Chr 16 @ 77 D16S3253/D16S5033.51 0.1 3.2 Chr 20 @ 62 D20S481/D20S1191.97 0.0 2.7

29. Summary The Lupus SCOR combined genome scan for SLE provides evidence of linkage to several chromosomal regions: 1q, 4p, 4q, 6, 7p, 16, 20 With the exception of chromosome 6, our linkage peaks tend to be dominated by the Caucasian pedigrees in our sample Several of our linkage signals appear to be supported by published genome scans Fine mapping efforts related to these linkage regions are underway within the SCOR as part of its mission to map and clone genes predisposing to SLE and related phenotypes

30. Genetic Mapping Fine Mapping Susceptibility Gene(s) ACGCCACC ACGTCACC DNA Phenotypes Diagnostic Tests New Mechanisms New Drugs Gene-Environment Interactions Genome Screening and Linkage Analyses Positional Cloning in Complex Diseases

31. Acknowledgements University of Alabama-Birmingham Robert P. Kimberly Jeffrey C. Edberg University of Minnesota Timothy W. Behrens Patrick M. Gaffney Robert R. Graham University of Oklahoma John B. Harley Jennifer H. Kelly Courtney Gray-McGuire Kathy L. Moser* Wake Forest University Stephen S. Rich W. Mark Brown Carl D. Langefeld